Publications containing results from models in this data release: --------------------------- Tiedeman, C.R., A.M. Shapiro, P.A. Hsieh, T.E. Imbrigiotta, D.J. Goode, P.J. Lacombe, M.F. DeFlaun, S.R. Drew, C.D. Johnson, J.H. Williams, G.P. Curtis, 2017, Bioremediation in Fractured Rock: 1. Modeling to Inform Design, Monitoring, and Expectations. Groundwater. doi: 10.1111/gwat.12585 Shapiro, A.M., C.R. Tiedeman, T.E. Imbrigiotta, D.J. Goode, P.A. Hsieh, P.J. Lacombe, M.F. DeFlaun, S.R. Drew, G.P. Curtis, 2017, Bioremediation in Fractured Rock: 2. Mobilization of Chloroethene Compounds from the Rock Matrix. Groundwater. doi: 10.1111/gwat.12586 Data Release: --------------------- Tiedeman, C.R., P.A. Hsieh, and A.M. Shapiro, 2017, MODFLOW-2005 and MT3DMS models used to design and evaluate a bioremediation experiment at the former Naval Air Warfare Center, West Trenton, NJ, http://dx.doi.org/10.5066/F71J97XV ---------------------------------------------------------------------------------------------------- Archive Revision History: ------------------------ 01/13/2017 Model archive created to conform to the structure specified for public release of groundwater flow and transport models. 02/07/2017 Model archive update based on USGS colleague review of model archive. 06/06/2017 Model archive update based on review comments on the articles by anonymous reviewers at the journal Groundwater. ---------------------------------------------------------------------------------- Tiedeman2017_Shapiro2017_Groundwater\ Description: ----------- The underlying directories contain all of the input and output files for the simulations described in the journal articles, and source code for MODFLOW-2005 (v1.11.0), MT3DMS (v5.30), MODPATH (v6.0), ZONEBUDGET (v.3.01), and ModelViewer (v.1.7). Descriptions of the data in each directory are given to facilitate understanding of this model archive. File descriptions are provided for selected files to provide additional information that may be of use for understanding this model archive. Support is provided for correcting errors in the data release and clarification of the modeling conducted by the U.S. Geological Survey. Users are encouraged to review the complete manuscripts of Tiedeman and others (2017) and Shapiro and others (2017) to understand the purpose, construction, and limitations of the models. ----------------------------------------------------------------------------------- Reconstructing the data release from the online data release: ------------------------------------------------------------- This data release is available from: http://dx.doi.org/10.5066/F71J97XV The models, along with post-processing tools, will run successfully only if the original directory structure is correctly restored. The data release is broken into several pieces to reduce the likelihood of download timeouts. Small files (readme.txt and modelgeoref.txt) are available as uncompressed files. All other files are zipped at the subdirectory level. For example, the files in the "georef" subdirectory are zipped into a zip file named "georef.zip". All zip files should be unzipped into a directory with the same name as the zip file name without the .zip extension. All zip files with names starting with "output" should be unzipped in the same manner as other zip files but should be placed within an "output" subdirectory created at the same level as the "georef" subdirectory created from "georef.zip". The highest-level directory structure of the original data release is: Tiedeman2017_Shapiro2017_Groundwater\ \ancillary\ Contains files for computing uncertainty of predicted fluxes \bin\ Contains binary executable files for MODFLOW-2005, MT3DMS, MODPATH, ZONEBUDGET, and ModelViewer \georef\ Contains ArcGIS shapefile of model grids \model\ Contains input files for MODFLOW-2005, MT3DMS, MODPATH,and ZONEBUDGET simulations \output\ Contains output files for MODFLOW-2005, MT3DMS, MODPATH,and ZONEBUDGET simulations \source\ Contains the source code files for MODFLOW-2005, MT3DMS (unmodified and modified versions), MODPATH, ZONEBUDGET, and ModelViewer To reconstruct the data release on the user's computer running the Windows operating system: Create a directory Tiedeman2017_Shapiro2017_Groundwater\. Download ancillary.zip, bin.zip, georef.zip, model.zip, output.zip, and source.zip from http://dx.doi.org/10.5066/F71J97XV. Unzip each of the zip files in the directory Tiedeman2017_Shapiro2017_Groundwater\, so that this directory contains the directories ancillary\, bin\, georef\, model\, output\, and source\. The contents of these directories are listed and described below. System requirements: -------------------- The flow models require approximately 400 to 800 MB of available Random Access Memory (RAM). The transport models require approximately 2.1 to 2.3 GB of RAM. The models have been run successfully on computers running the 64-bit Windows 7 operating system. Files: ----- readme.txt : This file, which documents the structure of the data release and instructions on how to run the models. modelgeoref.txt : ASCII file with the four corners of a rectangle encompassing the model domains. ancillary\ Description and Content: ----------- This directory contains the following directories: Uncertainty.ucode\ Contains all necessary files to run UCODE_2014 to calculate 95% confidence intervals for the estimated mixing zone fluxes described in Shapiro and others (2017). Output.Uncertainty.ucode\ Contains output from the UCODE runs. source\ Contains UCODE_2014 source code. To run UCODE for calculating uncertainty, execute the following three batch files sequentially: (1) 01-ucode.bat, (2) 02-ucode-prediction.bat, and (3) 03-LinUncertainty.bat. The runs in each batch file must be completed before the next batch file in the sequence is executed. These batch files are in the directory Uncertainty.ucode\. Further details about the files in the ancillary\ directory are provided in the file ancillary\_ReadMe_ancillary.txt. ZIP Files: --------- ancillary.zip bin\ Description: ----------- This directory contains binary executable files for MODFLOW-2005, MT3DMS, MODPATH, and ZONEBUDGET, which were used for all modeling analyses documented in Tiedeman and others (2017) and Shapiro and others (2017). ZIP Files: --------- bin.zip georef\ Description: ----------- This directory contains an ArcGIS shapefile defining the active areas of the models documented in Tiedeman and others (2017). ZIP Files: --------- georef.zip model\ Description: ----------- This directory contains all of the input files for the model runs described in Tiedeman and others (2017) and Shapiro and others (2017). These input files are contained in 16 separate numbered directories, listed below in the order in which the models are discussed in the two articles, and directory 'externalfiles' containing files common to more than one numbered directory: directories under model\ -------------------- 01_15BR_AqTest1.mf\ 02_45BR_AqTest1.mf\ 03_56BR_AqTest.mf\ 04_15BR_AqTest3.mf\ 05_45BR_AqTest2.mf\ 06_60BR_AqTest.mf\ 07_SteadyStateFlow_FlowModelGrid.mf\ 08_FluxesForBromideTransportModel.mf\ 09_BromideTransportModel.mt\ 10_BromideTransportModel_NoDiffusion.mt\ 11_SteadyStateFlow_TransportModelGrid.mf\ 12_Dilution.zonebudget\ 13_FluxesForTransportModelToDetermineMixingVolume.mf\ 14_TransportModelToDetermineMixingVolume.mt\ 15_DetermineBoundarySegments.modpath\ 16_MixingZoneFluxes.zonebudget\ externalfiles\ ZIP Files: --------- model.zip 01_15BR_AqTest1.mf\ 02_45BR_AqTest1.mf\ 03_56BR_AqTest.mf\ 04_15BR_AqTest3.mf\ 05_45BR_AqTest2.mf\ 06_60BR_AqTest.mf\ Description: ----------- These directories contain input files for the six aquifer test simulations described in the "Flow Models" section of Tiedeman and others (2017). Files unique to each simulation are in these directories, and files common to all six simulations are in directory externalfiles\. To run the model in each of these directories, run the batch file 'MF2005dbl.BAT'. This batch file runs the MODFLOW-2005 executable in the bin directory. 07_SteadyStateFlow_FlowModelGrid.mf\ Description: ----------- This directory contains input files for the steady state flow model used to simulate July 2008 head measurements that represent long-term average conditions, described in the "Flow Models" section of Tiedeman and others (2017). It uses a model grid in which the smallest cell sizes are 4 m x 4 m in the areal dimension. To run the model , execute the batch file 'MF2005dbl.BAT'. This batch file runs the MODFLOW-2005 executable in the bin directory. 08_FluxesForBromideTransportModel.mf\ Description: ----------- This directory contains input files for a flow model that simulates fluid stresses during the bromide tracer test described in the "Chemical Transport Properties and Residence Times" section of Tiedeman and others (2017). Additional input files for this flow model are in the directory externalfiles\. The simulated fluid stresses are described in the "Transport Model" section of Tiedeman and others (2017). This model uses a grid with cell sizes of 1 m x 1 m in the area where bromide transport is simulated. This grid is denoted the transport model grid. This model produces groundwater flow rates used as input for the MT3DMS transport model simulations in directories 09_BromideTransportModel.mt\ and 10_BromideTransportModel_NoDiffusion.mt\. To run the model, execute the batch file 'MF2005dbl.BAT'. This batch file runs the MODFLOW-2005 executable in the bin directory. 09_BromideTransportModel.mt\ Description: ----------- This directory contains input files for the transport model that simulates the bromide tracer test described in the "Chemical Transport Properties and Residence Times" section of Tiedeman and others (2017). The transport model is described in the "Transport Models" section of Tiedeman and others (2017). The MODFLOW run in 08_FluxesForBromideTransportModel.mf\ MUST be executed prior to running the MT3DMS model in 09_BromideTransportModel.mt\, because the nawc_rgn_trnsp.ftl file output from this MODFLOW run is an input file for the MT3DMS run. To run the MT3DMS model, execute the batch file 'mt3dms_dtoverride_x64_dbl.bat'. This batch file runs the MT3DMS executable mt3dms5b_dtoverride_x64_dbl.exe in the bin directory. 10_BromideTransportModel_NoDiffusion.mt\ Description: ----------- This directory contains input files for the bromide transport simulation described in the "Simulated Bromide Transport" section of Tiedeman and others (2017). The MODFLOW run in 08_FluxesForBromide TransportModel.mf\ MUST be executed prior to running the MT3DMS model in 10_BromideTransportModel_NoDiffusion.mt\, because the nawc_rgn_trnsp.ftl file output from this MODFLOW run is an input file for the MT3DMS run. To run the MT3DMS model, execute the batch file 'mt3dms_dtoverride_x64_dbl.bat'. This batch file copies the nawc_rgn_trnsp.ftl file from 08_FluxesForTransportModel.mf\ to 10_BromideTransportModel_NoDiffusion.mt\ and then executes the MT3DMS executable mt3dms5b_dtoverride_x64_dbl.exe in the bin directory. To visualize simulated concentrations, execute ModelViewer_x64_dbl.bat, which runs the ModelViewer executable in directory source\ModelViewer_x64_dbl\. In ModelViewer go to File --> Open and open Conc_Fig8.mv. Use the controls in Toolbox --> Grid --> Subgrid to examine concentration in different layers and in Toolbox --> Animation to examine concentration at different times. In the Subgrid dialog box, setting k=20 shows model layer 14, and setting k=22 shows model layer 22. 11_SteadyStateFlow_TransportModelGrid.mt\ Description: ----------- This directory contains input files for the steady state flow model used to simulate July 2008 head measurements that represent long-term average conditions, described in the "Flow Models" section of Tiedeman and others (2017). It uses the transport model grid, in which the smallest cell sizes are 1 m x 1 m in the areal dimension. Additional input files for this flow model are in the directory externalfiles\. To run the model, execute the batch file 'MF2005dbl.BAT'. This batch file executes the MODFLOW-2005 executable in the bin directory. 12_Dilution.zonebudget\ Description: ----------- This directory contains input files for two ZONEBUDGET simulations. The MODFLOW run in 11_SteadyStateFlow_TransportModelGrid.mf\ MUST be executed prior to running ZONEBUDGET because the nawc_rgn_trnsp_stst.bud file output from this MODFLOW run is an input file for the ZONEBUDGET runs. One ZONEBUDGET simulation calculates fluxes described in the "Expected Extent of Treatment Zone" section of Tiedeman and others (2017). To run ZONEBUDGET, execute the batch file 'ZoneBud_Dilution_VerticalFracture.BAT'. The other ZONEBUDGET simulation calculates fluxes described in the "Monitoring Strategy" section of Tiedeman and others (2017). To run ZONEBUDGET, execute the batch file 'ZoneBud_Dilution_45BR.BAT'. The batch files run the ZONEBUDGET executable in the bin\ directory. The file '_ReadMe_Dilution.txt' describes the zones defined for each of the ZONEBUDGET simulations. 13_FluxesForTransportModelToDetermineMixingVolume.mf\ Description: ----------- This directory contains input files for a flow model that simulates fluid stresses during the injection of bioremediation amendments and flush water described in the "Injection of Remediation Amendments" section of Shapiro and others (2017). This model is discussed in the "Mixing Volume and Groundwater Fluxes" section of Shapiro and others (2017). This model provides groundwater flow rates used as input for the MT3DMS simulation to determine the extent of the mixing volumes. Additional input files for this flow model are in the directory externalfiles\. To run the model, execute the batch file 'MF2005dbl.BAT'. This batch file executes the MODFLOW-2005 executable in the bin\ directory. 14_TransportModelToDetermineMixingVolume.mt\ Description: ----------- This directory contains input files for the transport model used to simulate the mixing volumes defined by C/C0 concentration ratios of 1e-04 and 1e-06, described in the "Mixing Volume and Groundwater Fluxes" section of Shapiro and others (2017). The injection concentration for these runs is set to 1000. The MODFLOW run in 13_FluxesForTransportModelToDetermineMixingVolume.mf\ MUST be executed prior to running the MT3DMS model in 14_TransportModel_DetermineMixingVolume.mt\, because the nawc_rgn_trnsp.ftl file output from this MODFLOW run is an input file for the MT3DMS run. To run the model, execute the batch file 'mt3dms_x64_dbl.bat'. This batch file copies the nawc_rgn_trnsp.ftl file from 13_FluxesForTransportModelToDetermineMixingVolume.mf\ to 14_TransportModelToDetermineMixingVolume.mt\ and then executes the MT3DMS executable mt3dms5b_x64_dbl.exe in the bin\ directory. To visualize a mixing volume, execute ModelViewer_x64_dbl.bat, which runs the ModelViewer executable in directory source\ModelViewer_x64_dbl\. In ModelViewer go to File --> Open and open CdivC0_1e-4.mv or CdivC0_1e-6.mv. Go to Toolbox --> Animation, and under "Set to time", select the final time listed. Under Toolbox --> Solid, the "Min Value" has been set to 0.1 in file CdivC0_1e-4.mv, which equals 1000 x 1e-04, and has been set to 0.001 in file CdivC0_1e-4.mv, which equals 1000 x 1e-06. With these specified values, the mixing volumes defined by a contours of C/C0 = 1e-04 and C/C0 = 1e-06 are shown in, respectively, CdivC0_1e-4.mv and CdivC0_1e-4.mv. Bitmaps of the volumes are provided in files MixingVolumeCdivC0_1e-4.bmp and MixingVolumeCdivC0_1e-6.bmp. 15_DetermineBoundarySegments.modpath\ Description: ----------- This directory contains input files for the MODPATH simulations used to identify segments of the mixing volume boundary where groundwater enters and exits, as described in the "Mixing Volume and Groundwater Fluxes" section of Shapiro and others (2017). Files with the string "CdivC0_1e-04" in the name are those for determining the mixing volume associated with a C/C0 concentration ratio of 1e-04. Files with the string "CdivC0_1e-06" in the name are those for determining the mixing volume associated with a C/C0 concentration ratio of 1e-06. Files with the string "backward" in the name are for backward tracking of particles starting in the mixing volume, to determine the location of fluid flow entering the mixing volume. Files with the string "forward" in the name are for forward tracking of particles starting in the mixing volume, to determine the location of fluid flow exiting the mixing volume. The MODFLOW run in 11_SteadyStateFlow_TransportModelGrid.mf\ MUST be executed prior to running the MODPATH simulations in 15_DetermineBoundarySegments.modpath\, because the nawc_rgn_trnsp_stst.bud and nawc_rgn_trnsp_stst.bhd files output from this MODFLOW run are input files for the MODPATH runs. To run the backward and forward particle tracking simulations for both mixing volumes, execute the four batch files that have the suffix '.BAT': mpath6.CdivC0_1e-4_Boundary.backward.BAT mpath6.CdivC0_1e-4_Boundary.forward.BAT mpath6.CdivC0_1e-6_Boundary.backward.BAT mpath6.CdivC0_1e-6_Boundary.forward.BAT These batch files run the MODPATH executable in the bin\ directory. To visualize the particle tracks, execute ModelViewer_x64_dbl.bat, which runs the ModelViewer executable in directory source\ModelViewer_x64_dbl\. In ModelViewer go to File --> Open and open one of the following files: ParticleTrack_CdivC0_1e-4_Boundary.backward.mv ParticleTrack_CdivC0_1e-4_Boundary.forward.mv ParticleTrack_CdivC0_1e-6_Boundary.backward.mv ParticleTrack_CdivC0_1e-6_Boundary.forward.mv For the forward particle tracking visualizations, the starting point of each particle path is at the blue end of the path. Bitmaps showing the paths are provided in files: ParticleTrack_CdivC0_1e-4_Boundary.backward.bmp ParticleTrack_CdivC0_1e-4_Boundary.forward.bmp ParticleTrack_CdivC0_1e-6_Boundary.backward.bmp ParticleTrack_CdivC0_1e-6_Boundary.forward.bmp 16_MixingZoneFluxes.zonebudget\ Description: ----------- This directory contains input files for the ZONEBUDGET simulations to calculate fluxes entering and exiting the mixing volumes described in the "Mixing Volume and Groundwater Fluxes" section of Shapiro and others (2017). Files with the string "CdivC0_1e-04" in the name are for calculating fluxes for the mixing volume associated with a C/C0 concentration ratio of 1e-04. Files with the string "CdivC0_1e-06" in the name are for calculating fluxes for the mixing volume associated with a C/C0 concentration ratio of 1e-06. The MODFLOW run in 11_SteadyStateFlow_TransportModelGrid.mf\ MUST be executed prior to running the ZONEBUDGET model in 16_MixingZoneFluxes.zonebudget\, because the nawc_rgn_trnsp_stst.bud file output from this MODFLOW run is an input file for the ZONEBUDGET run. To run ZONEBUDGET, run the two batch files ZoneBud_CdivC0_1e-4_Boundary.BAT and ZoneBud_CdivC0_1e-6_Boundary.BAT. These batch files execute the ZONEBUDGET executable in the bin\ directory. The file '_ReadMe_MixingZoneFluxes.txt' describes the zones defined for the calculations. output\ Description: ----------- This directory contains all of the output files for the simulations in the 16 numbered directories under model\ directories under output\ -------------------- output.01_15BR_AqTest1.mf\ output.02_45BR_AqTest1.mf\ output.03_56BR_AqTest.mf\ output.04_15BR_AqTest3.mf\ output.05_45BR_AqTest2.mf\ output.06_60BR_AqTest.mf\ output.07_SteadyStateFlow_FlowModelGrid.mf\ output.08_FluxesForBromideTransportModel.mf\ output.09_BromideTransportModel.mt\ output.10_BromideTransportModel_NoDiffusion.mt\ output.11_SteadyStateFlow_TransportModelGrid.mf\ output.12_Dilution.zonebudget\ output.13_FluxesForTransportModelToDetermineMixingVolume.mf\ output.14_TransportModelToDetermineMixingVolume.mt\ output.15_DetermineBoundarySegments.modpath\ output.16_MixingZoneFluxes.zonebudget\ ZIP Files: ---------- output.zip source\ Description: ----------- This directory contains the source code files for MODFLOW-2005 v1.11.0, MT3DMS v5.30, MODPATH v6.0, ZONEBUDGET v.3.01, and ModelViewer v1.7. Notes on MT3DMS: Modified and unmodified versions of MT3DMS are provided. The unmodified version is in directory mt3dms5b\ and the modified version is in directory mt3dms5b_modify_dt\, which contains file _ReadMe_Modify_dt.txt explaining the modifications. The modified version implements a method for increasing the MT3DMS-calculated time step size, resulting in reduced runtimes. This change has been tested only for simulations in which velocities at a pumping well are substantially larger than elsewhere in the model domain. The modified version of MT3DMS is used for transport simulations in directories 09_BromideTransportModel.mt and 10_BromideTransportModel_NoDiffusion. The unmodified version of MT3DMS is used for the transport simulation in directory 14_TransportModel_DetermineMixingVolume. Notes on ModelViewer: The version of ModelViewer provided is a version from 2014 that was modified to run on 64-bit operating systems, and to read in double precision MODFLOW and MT3DMS output files. This version must be used for the visualizations described in this readme.txt files. Later versions may not be compatible with the .ftl files produced by the MODFLOW versions used in the simulations in this archive. ZIP Files: --------- source.zip